wip: toward a builder patter for metadata configurations

src/main/java/org/janelia/saalfeldlab/n5/config/AbstractConfigurationBuilder.java

@@ -0,0 +1,23 @@
+package org.janelia.saalfeldlab.n5.config;
+
+import org.janelia.saalfeldlab.n5.metadata.MetadataHierarchyWriter;
+
+public abstract class AbstractConfigurationBuilder implements ConfigurationBuilder {
+
+	protected Parameters parameters;
+
+	public AbstractConfigurationBuilder() {
+
+		parameters = new Parameters();
+	}
+
+	@Override
+	public Parameters getParameters() {
+
+		return parameters;
+	}
+
+	@Override
+	public abstract MetadataHierarchyWriter getWriter();
+
+}

src/main/java/org/janelia/saalfeldlab/n5/config/ConfigurationBuilder.java

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+package org.janelia.saalfeldlab.n5.config;
+
+import java.util.Map;
+import java.util.function.IntFunction;
+import java.util.stream.IntStream;
+
+import org.janelia.saalfeldlab.n5.Compression;
+import org.janelia.saalfeldlab.n5.DataType;
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.N5Exception;
+import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+import org.janelia.saalfeldlab.n5.metadata.MetadataHierarchyWriter;
+import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
+
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.cell.AbstractCellImg;
+import net.imglib2.img.cell.CellImg;
+import net.imglib2.type.NativeType;
+
+public interface ConfigurationBuilder {
+
+	public Parameters getParameters();
+
+	public MetadataHierarchyWriter getWriter();
+
+	public default ConfigurationBuilder image(
+			final RandomAccessibleInterval<? extends NativeType<?>> img,
+			final Axis[] axes) {
+
+		dataType((NativeType<?>)img.getType());
+		dimensions(img.dimensionsAsLongArray());
+		numChannels(img, axes);
+		numTimepoints(img, axes);
+
+		if (img instanceof CellImg) {
+			AbstractCellImg<?, ?, ?, ?> cellimg = (AbstractCellImg<?, ?, ?, ?>)img;
+			blockSize(cellimg.getCellGrid().getCellDimensions());
+		}
+
+		return this;
+	}
+
+	public default ConfigurationBuilder dimensions(final long... dimensions) {
+
+		getParameters().dimensions = dimensions;
+		return this;
+	}
+
+	public default ConfigurationBuilder blockSize(final int... blockSize) {
+
+		getParameters().blockSize = blockSize;
+		return this;
+	}
+
+	public default ConfigurationBuilder dataType(final DataType dataType ) {
+
+		getParameters().dataType = dataType;
+		return this;
+	}
+
+	public default ConfigurationBuilder dataType(@SuppressWarnings("rawtypes") final NativeType type ) {
+
+		@SuppressWarnings("unchecked")
+		final DataType dtype = N5Utils.dataType(type);
+		if (dtype != null)
+			dataType(dtype);
+
+		return this;
+	}
+
+	public default ConfigurationBuilder compression(final Compression compression ) {
+
+		getParameters().compression = compression;
+		return this;
+	}
+
+	public default ConfigurationBuilder resolution(final double... resolution) {
+
+		getParameters().resolution = resolution;
+		return this;
+	}
+
+	public default ConfigurationBuilder offset(final double... offset) {
+
+		getParameters().offset = offset;
+		return this;
+	}
+
+	public default ConfigurationBuilder unit(final String... units) {
+
+		getParameters().units = units;
+		return this;
+	}
+
+	public default ConfigurationBuilder numChannels(final int numChannels) {
+
+		getParameters().numChannels = numChannels;
+		return this;
+	}
+
+	public default ConfigurationBuilder multichannelGroups(final IntFunction<String> relativeChannelGroupName) {
+
+		getParameters().relativeChannelGroupName = relativeChannelGroupName;
+		return this;
+	}
+
+	public default ConfigurationBuilder multichannelGroups(final String... relativeChannelGroupNames) {
+
+		getParameters().relativeChannelGroupName = c -> relativeChannelGroupNames[c];
+		return this;
+	}
+
+	public default ConfigurationBuilder multichannelGroups(final Map<Integer,String> relativeChannelGroupNames) {
+
+		getParameters().relativeChannelGroupName = c -> relativeChannelGroupNames.get(c);
+		return this;
+	}
+
+	public default ConfigurationBuilder numScales(final int numScales) {
+
+		getParameters().numScales = numScales;
+		return this;
+	}
+
+	public default ConfigurationBuilder multiscaleGroups(final IntFunction<String> relativeScaleLevelGroupName) {
+
+		getParameters().relativeScaleLevelGroupName = relativeScaleLevelGroupName;
+		return this;
+	}
+
+	public default ConfigurationBuilder multiscaleGroups(final String... relativeScaleLevelGroupName) {
+
+		getParameters().relativeScaleLevelGroupName = c -> relativeScaleLevelGroupName[c];
+		return this;
+	}
+
+	public default ConfigurationBuilder multiscaleGroups(final Map<Integer, String> relativeScaleLevelGroupName) {
+
+		getParameters().relativeScaleLevelGroupName = s -> relativeScaleLevelGroupName.get(s);
+		return this;
+	}
+
+	public default ConfigurationBuilder downsampleFactors(IntFunction<int[]> downsamplingFactors) {
+
+		getParameters().downsamplingFactors = downsamplingFactors;
+		return this;
+	}
+
+	public default ConfigurationBuilder downsampleFactors(int[][] downsamplingFactors) {
+
+		getParameters().numScales = downsamplingFactors.length;
+		getParameters().downsamplingFactors = s -> downsamplingFactors[s];
+		return this;
+	}
+
+	public default DatasetAttributes getBaseDatasetAttributes() {
+
+		return new DatasetAttributes(
+				getParameters().dimensions,
+				getParameters().blockSize,
+				getParameters().dataType,
+				getParameters().compression);
+	}
+
+	public static long numChannels(final RandomAccessibleInterval<? extends NativeType<?>> img, final Axis[] axes) {
+
+		return countElementsOfType(img, axes, Axis.CHANNEL);
+	}
+
+	public static long numTimepoints(final RandomAccessibleInterval<? extends NativeType<?>> img, final Axis[] axes) {
+
+		return countElementsOfType(img, axes, Axis.SPACE);
+	}
+
+	public static long countElementsOfType(final RandomAccessibleInterval<? extends NativeType<?>> img, final Axis[] axes, final String type) {
+
+		final int[] indexes = IntStream.range(0, axes.length)
+				.filter(i -> axes[i].getType().equals(type))
+				.toArray();
+		if (indexes.length == 1)
+			throw new N5Exception(String.format("Multiple %s axes detected, but only one allowed", type));
+		else if (indexes.length == 1)
+			return img.dimension(indexes[0]);
+		else
+			return 1;
+	}
+
+}

src/main/java/org/janelia/saalfeldlab/n5/config/N5ViewerBuilder.java

@@ -0,0 +1,48 @@
+package org.janelia.saalfeldlab.n5.config;
+
+import org.janelia.saalfeldlab.n5.N5Exception;
+import org.janelia.saalfeldlab.n5.metadata.N5ViewerMultiscaleHierarchyWriter;
+import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils;
+
+import net.imglib2.img.cell.CellImgFactory;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+
+public class N5ViewerBuilder extends AbstractConfigurationBuilder {
+
+	public N5ViewerBuilder() {
+
+		super();
+	}
+
+	@Override
+	public N5ViewerMultiscaleHierarchyWriter getWriter() {
+
+		// TODO check that all units are equal?
+		return N5ViewerMultiscaleHierarchyWriter.build(
+				getParameters().numChannels,
+				getBaseDatasetAttributes(),
+				getParameters().numScales,
+				getParameters().resolution,
+				getParameters().units[0],
+				getParameters().downsamplingFactors);
+	}
+
+	@Override
+	public ConfigurationBuilder offset(final double[] offset) {
+
+		throw new N5Exception("N5Viewer does not support offset");
+	}
+
+	public static void main(String[] args) {
+
+		final N5ViewerBuilder builder = new N5ViewerBuilder();
+		builder.image(
+				new CellImgFactory<UnsignedByteType>(new UnsignedByteType()).create(4, 3, 2),
+				AxisUtils.buildAxes("x", "y", "z"));
+		System.out.println(builder.parameters);
+
+		// throws exception
+		// builder.offset(new double[]{2, 3, 4});
+	}
+
+}

src/main/java/org/janelia/saalfeldlab/n5/config/Parameters.java

@@ -0,0 +1,51 @@
+package org.janelia.saalfeldlab.n5.config;
+
+import java.util.Arrays;
+import java.util.function.IntFunction;
+
+import org.janelia.saalfeldlab.n5.Compression;
+import org.janelia.saalfeldlab.n5.DataType;
+import org.janelia.saalfeldlab.n5.GzipCompression;
+
+public class Parameters {
+
+	// single (base) dataset
+	public long[] dimensions;
+	public int[] blockSize;
+	public DataType dataType;
+	public Compression compression = new GzipCompression();
+
+	// spatial and time resolution 
+	public double[] resolution;
+	public double[] offset;
+	public String[] units;
+
+	// multichannel
+	public int numChannels = 1;
+	public IntFunction<String> relativeChannelGroupName = c -> String.format("c%d", c);
+
+	// multiscale
+	public int numScales;
+	public IntFunction<String> relativeScaleLevelGroupName = s -> String.format("s%d", s);
+	public IntFunction<int[]> blockSizePerScaleLevel = s -> blockSize;
+	public IntFunction<int[]> downsamplingFactors = s -> {
+		final int[] factors = new int[dimensions.length];
+		Arrays.fill(factors, (int)Math.pow(2, s));
+		return factors;
+	};
+
+	public String toString() {
+
+		return String.format(
+				"dimensions : %s\n" +
+				"dataType : %s\n" +
+				"blockSize : %s\n" +
+				"resolution : %s\n" +
+				"offset : %s\n",
+				Arrays.toString(dimensions),
+				dataType,
+				Arrays.toString(blockSize),
+				Arrays.toString(resolution),
+				Arrays.toString(offset));
+	}
+}

src/main/java/org/janelia/saalfeldlab/n5/metadata/DatasetUtils.java

@@ -0,0 +1,42 @@
+package org.janelia.saalfeldlab.n5.metadata;
+
+import java.util.function.IntFunction;
+import java.util.function.Supplier;
+import java.util.stream.IntStream;
+
+import org.janelia.saalfeldlab.n5.Compression;
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+import org.janelia.scicomp.n5.zstandard.ZstandardCompression;
+
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.NativeType;
+
+public class DatasetUtils {
+
+	public static <T extends NativeType<T>> DatasetAttributes defaultDatasetAttributes(
+			final RandomAccessibleInterval<T> img ) {
+
+		return datasetAttributes(img,
+				() -> IntStream.generate(() -> 64).limit(img.numDimensions()).toArray(),
+				ZstandardCompression::new);
+	}
+
+	public static <T extends NativeType<T>> DatasetAttributes datasetAttributes(
+			final RandomAccessibleInterval<T> img,
+			final Supplier<int[]> blockSize,
+			final Supplier<Compression> compression) {
+
+		return new DatasetAttributes(
+				img.dimensionsAsLongArray(),
+				blockSize.get(),
+				N5Utils.dataType(img.getType()),
+				compression.get());
+	}
+
+	public static IntFunction<int[]> toFunction(int[][] arr) {
+
+		return i -> arr[i];
+	}
+
+}

src/main/java/org/janelia/saalfeldlab/n5/metadata/MetadataHierarchyWriter.java

@@ -0,0 +1,9 @@
+package org.janelia.saalfeldlab.n5.metadata;
+
+import org.janelia.saalfeldlab.n5.N5Writer;
+
+public interface MetadataHierarchyWriter {
+
+	public void write(final N5Writer n5, final String baseDataset);
+
+}